Why does geometry deform in unexpected ways when using IK?
This is a common occurrence when I set-up IK, I often set the pole angle to 90 degrees (sometimes 180 degrees) to fix the direction the knee points. I suspect it has to do with the orientation of the joints that are pointing to the pole in relation to the orientation of the pole itself.

However, because you can simply apply a correction to the constraint, I don't see much need to think over it further than that. There shouldn't be any problems with animation or posing due to requiring an offset to the pole angle in the constraint. So no need to worry about it ^_^

Edit: I just saw your edit. You should check that your skeleton is symmetrical on both sides. I've had angle issues like this before when the pole OR the leg joints were off by even a fraction of a unit. You need to make sure that your extruded pole joint is directly in front of (ie: same x-location) your knee joint.